PLABO

Tuesday, 15 August 2017

Change Docker default software dir

For Docekr 17.xx in Ubuntu 16.04 don't follow the advice of updating the /etc/default/docker and change -g option in DOCKER_OPTS. This advice is for OLD debian using upstar system. If your linux uses Systemd do the following: use the /etc/docker/daemon.json and add a graph directive

Monday, 10 October 2016

RDP is more efficient and has better performing than VNC and probably is more secure.

Installation

The adventage of x11vnc is that you have the same desktop that is open in your workstation and two persons can share the screen. The cons is that you need to have a logged user in the Xs before using it. If you restart the
machine then you need to do some tricks to us x11vnc as root to be able
to go to the splash window.

XRDP is better but by default you open different sessions each time and is not trivial how to get the current session active in your workstation.

Anyway, if you use Centos7 you will have probles usig XRDP because there are some issues with selenux (the security system for applications in redhat)

But the job is not finished. By default XRDP listen to 3389 but this service is not allowed to listen to this port by default. You need to fix security and firewall to allow XRDP listen to 3389 (selenux) and allow external connections to 2289 (firewall)

Saturday, 13 February 2016

Seems that Iddle fingers, Mervibore soft,Twilight and Tomorrow Night have the softest color schema with good contrast for comments and not to bright colours for the long coding nights ahead. I like the comments in italic and with not a prominent color (I want to keep my attention at the code) so Twilight is my current chose.

Sunday, 31 January 2016

Installing MySQL, mysqlworkbench and mysql-utils in Yosemite

For installing things like *nix in MacOSX I use homebrew.

Homebrew is fantastic for installing tar.gz files in textual way, but there are some packages that are only in .dmg format and you need to use a package manager that knows how to install this GUI based installers. This package manager is homebrew cask (caskroom project)

POODLE affects SSLv3 or version 3 of the Secure Sockets Layer protocol, which is used to encrypt traffic between a browser and a web site or between a user’s email client and mail server. It’s not as serious as the recent Heartbleed and Shellshock vulnerabilities, but POODLE could allow an attacker to hijack and decrypt the session cookie that identifies you to a service like Twitter or Google, and then take over your accounts without needing your password.

According to the team's Bodo Möller: "This vulnerability allows the plaintext of secure connections to be calculated by a network attacker."

This is a client security hole. This is a vulnerability in the old SSLv3 (relaying in 80's code), but even if you have all set for using TLS, in many applications the server can trick you to downgrade to SSL and then it can stole you some security cookies.

This vulnerability is a risk in public wifi but not at home or work.

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Mozilla says that it is making Firefox 34 safe from POODLE by disabling SSL 3.0 by default. The code which does this is already baked into the Nightly channel, and will make its way to the Aurora and Beta channels also "in the next few weeks".

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MicroSoft Advisory and Workarounds:

https://technet.microsoft.com/en-us/library/security/3009008.aspx
This workaround involves Group Policy Editor. For those using versions of Windows that don't include GPE simply go to Control Panel/Internet Options/Advanced/Security and uncheck the box for SSL 3.0 (SSL 2.0 should already be unchecked).

Thursday, 7 August 2014

In emacs you select text marking a starting selection point with control-space. This is a fundamental key binding in emacs. Now in the new version of Ubuntu (14.04) the default service for controlling multilingual input in linux has been changed to Ibus. The issue is that Ibus default key binding to control-space.

If you want to use emacs you probably should change this to something else. Go to a terminal and write 'ibus-setup' and at the right of the input method line you will find three dots '...' click there and change your key binding to Ibus pressing in the three dots in the key code line and then clik in disable. The text will change to 'new accelerator', press your combination of keys and you are done. I have changed mine to super-alt-space (super is the windows key).

Thursday, 27 February 2014

In bioinformatcis, bgzip files are important for random access to big files . Bgzip is a program modified from gzip program that uses block compression and is fully backwards compatible with gzip.
But I have issues when using bgzip compressed vcf files with Perl scripts that uses IO::Uncompress::Gunzip (that I believe it uses zlib under the hood). A similar problem happen to my recently with snpeff program (Java). In both cases the data is decompressed but truncated after a few hundred lines aprox.
I could be totally wrong but I was wondering if zlib (or whatever gzip compatible library they are using) is getting confused with the bgzip bloks and only processing one or a few of them leaving the output incomplete.
perl code that does not work:

I googled about and I was unable to find quickly any relevant entry, but this is something that I am sure other people would have already faced. Do someone have a clue about why is this happening? I am using ubuntu 12.04.4 with perl 5.16

[UPDATE 2014-02-28]: finally a clue come from biostars where Heng Li remind me a footnote in the SAM specs about a java library for gzip that only sees first block of bgzip when decompressing. Seems that Perl gzip implementations had the same problem.

Now you only need to open a file ended with .gpg and automatically emacs would ask you for the pasword for decryption and again for saving. No unencrypted temporary files are stored, or at least I am not aware of them.

Tuesday, 20 August 2013

In our sequencing facility we have processed 4 illumina 450K methylation chips for the same study at 2 diferent times. We took care of spreading case and controls among all the chips. We can see a clear time-of-processing batch effect:

The chips were run in two different days one month apart. first 24 samples and then the other 24 samples.

The negative controls of the second batch have a wider range.

And wen looking at the MDS and PCA we can see that the main parameter for grouping samples is the run day (the two chips starting with 835... where done the same day and the other two another day)

I have used the nice rnbeads R package for reporting the batch effects.

Now I am exploring two methods of correcting the batch effect:

limma using the batch date as block effect

design <- model.matrix(~Block+Treatment)

ComBat in the R SVA package for correcting this

I will post the results soon. Meanwhile any comment for dealing with batch effects in 450K chips is more than wellcome.